Objective To compare the accuracy of computer assisted total knee arthroplasty (TKA) and conventional positioning TKA for restoration of lower-extremity mechanical axis. Methods A prospective study for 40 patients who underwent TKA from January 2012 to June 2013 was conducted. Patients were randomly divided into the conventional surgery (CS) group (n=20) and the navigation surgery (NS) group (n=20). For the CS group, there were 7 male patients and 13 female patients with average age of (62.4±6.9) years and the conventional positioning TKA was adopted. For the NS group, there were 9 male patients and 11 female patients with average age of (63.6±8.7) years and the computer assisted TKA was adopted. Patients of both groups used the same brand of joint prostheses and all surgeries were performed by the same surgeon. The operation time, 24-hour drainage volume, the HSS scores 1 month and 6 months after the surgery, knee flexion, and lowerextremity mechanical axis angle of two groups were compared. Results The average operation time of the NS group was longer than that of the CS group (t=3.273, P=0.019), but 24-hour drainage volume of NS group was less than that of the CS group (t=2.156, P=0.031). The HSS scores and the average knee flexion of the NS group 1 month after the surgery were higher than those of the CS group and the differences were statistically significant (P<0.05). The differences of the HSS scores of the two groups 6 months after the surgery were not statistically significant (P>0.05). The average knee flexion of the NS group was larger than that of the CS group (t=1.232, P=0.047). The postoperative lower-extremity mechanical axis angle of the NS group (0.87°±0.92°) was closer to 0° than that of the CS group (1.93°±1.37°) and the difference was statistically significant (t=2.756, P=0.025). The difference of the angle between joint prosthesis and lower-extremity mechanical axis of two groups was not statistically significant (P>0.05). Conclusion The computer assisted TKA is more accurate than the conventional positioning TKA for the restoration of lower-extremity mechanical axis.